The accuracy of flood inundation maps is determined by the uncertainty propagated from all variables involved in the overall process including input data, model parameters and modeling approaches. This study investigated the uncertainty arising from key variables (flow condition and Manning’s n) among model variables in flood inundation mapping for the Missouri River near Boonville, Missouri, USA. Methodology of this study involves the generalized likelihood uncertainty estimation (GLUE) to quantify the uncertainty bounds of flood inundation area. Uncertainty bounds in the GLUE procedure are evaluated by selecting two likelihood functions, which is two statistic (inverse of sum of squared error (1/SAE) and inverse of sum of absolute error (1/SSE)) based on an observed water surface elevation and simulated water surface elevations. The results from GLUE show that likelihood measure based on 1/SSE is more sensitive on observation than likelihood measure based on 1/SAE, and that the uncertainty propagated from two variables produces an uncertainty bound of about 2% in the inundation area compared to observed inundation. Based on the results obtained form this study, it is expected that this study will be useful to identify the characteristic of flood.